Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ATAC-Seq)

ABSTRACT: Epigenetic modification plays a key role in the vernalization process and maintains gene expression states after low temperature. In this study, the Chinese main cultivar Aikang58 was used to construct the chromatin accessibility maps, expression profile and histone modification (including H3K27me3, H3K27ac, H3K36me3 and H3K4me3) maps of winter wheat before and after vernalization. We provided a crucial data resource for deep understanding of epigenome in vernalization. What’s more, important core regulatory elements and corresponding transcription factors were discovered, and the complex regulatory network of wheat vernalization was analyzed. ATAC-seq of leaf, axillary bud and shoot apex before and after vernalization

ORGANISM(S): Triticum aestivum

PROVIDER: GSE232424 | GEO | 2024/07/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (RNA-Seq)

Project description:Epigenetic modification plays a key role in the vernalization process and maintains gene expression states after low temperature. In this study, the Chinese main cultivar Aikang58 was used to construct the chromatin accessibility maps, expression profile and histone modification (including H3K27me3, H3K27ac, H3K36me3 and H3K4me3) maps of winter wheat before and after vernalization. We provided a crucial data resource for deep understanding of epigenome in vernalization. What’s more, important core regulatory elements and corresponding transcription factors were discovered, and the complex regulatory network of wheat vernalization was analyzed.

2024-07-22 | GSE232428 | GEO

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ChIP-Seq)

2024-07-22 | GSE232426 | GEO

Dynamic Yin-Yang regulation network of O-GlcNAcylation and phosphorylation mediates vernalization response for flowering in winter wheat

Project description:Protein post-translational modification (PTM) increases the functional diversity of the proteome and regulates numerous biological processes in eukaryotes. Two types of PTMs, O-linked-acetyl glucosamine modification (O-GlcNAc) and phosphorylation have been identified on the same amino acid, are considered as Yin-Yang modification for their antagonistic function recently. Vernalization, a prolonged cold exposure promoted flowering, is important for grain yield in temperate cereals, such as winter wheat. O-GlcNAcylation on TaGRP2 and phosphorylation on VER2 are involved in regulation of vernalization response (VRN) genes. However, less is known about how plant senses vernalization with general Yin-Yang modifications. Here we report that altering O-GlcNAc signaling by chemical inhibitors could change the vernalization response and affect flowering transition. Furthermore, we enriched O-GlcNAcylated and phosphorylated peptides from winter wheat plumules at different processing time points during vernalization by Lectin weak affinity chromatography (LWAC) and iTRAQ-TiO2, respectively. In total, about 200 O-GlcNAcylated proteins and 124 differential expressed phosphorylated proteins were identified by Mass Spectrum (MS). Based on GO enrichment, the identified O-GlcNAcylated proteins are mainly involved in response to abiotic stimulus and hormone, metabolic processing and gene expression. While dynamic phosphorylated proteins during vernalization participate in translation, transcription and metabolic processing. Of note, 31 proteins with both phosphorylation and O-GlcNAcylation modification were identified. Among them, TaGRP2 was further confirmed to participate in regulation of vernalization promoted flowering. The global modification profiles and genetic data at specific regulator suggested that the dynamic network of O-GlcNAcylation and phosphorylation on the key nodes regulate vernalization response and mediate flowering in wheat.

2020-12-18 | PXD008285 | Pride

Dynamic Yin-Yang regulation network of O-GlcNAcylation and phosphorylation mediatesvernalization response for flowering in winter wheat, part 2

2021-05-18 | PXD008298 | Pride

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-07-22 | GSE232430 | GEO

RNAseq analysis of Arabis alpina buds in the dormant zone (V2) and buds in the growing zone (V3) at the end of vernalization (+0) and 5 days later (+5d)

Project description:Arabis alpina, similar to woody perennials, has a complex architecture with a zone of axillary vegetative branches and a zone of dormant buds that serve as perennating organs. We show that floral development during vernalization is the key for shaping the dormant bud zone by facilitating a synchronized and rapid growth after vernalization and thereby causing an increase in auxin transport, response and endogenous indole-3-acetic acid (IAA) levels in the stem. Floral development during vernalization is associated with the development of axillary buds in subapical nodes. Our transcriptome analysis indicated that these buds are not dormant during vernalization but only reach sustained growth after the return to warm temperatures. Floral and subapical vegetative branches grow after vernalization and inhibit the development of the buds below. Dormancy in these buds is regulated across the A. alpina life cycle by low temperatures and by apical dominance in a BRANCHED 1 dependent mechanism.

2020-03-01 | GSE126944 | GEO

Genome-wide profiling of H3K4me3 and H3K27me3 modifications during and after vernalization in Brachypodium

Project description:Vernalization, the requirement of long-term exposure to low environmental temperature for flowering, is a typical epigenetic phenomenon in plants. Histone modifications have been analyzed for key vernalization genes, but genome-wide regulation remains unclear. Here, we performed global analysis of histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) trimethylation with Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) during and after vernalization to obtain complete view of histone modification fluctuation both on whole genome scale and for single genes, even different regions of genes. The critical role of H3K27me3 was revealed. During vernalization H3K27me3 regulation concentrated on a few biological processes, with two essential environmental responses, transcription regulation and anti-stress reactions, being main targets, as indicated by change pattern and GO analysis. The regulation of H3K4me3, however, showed no obvious focus. For gene expression, H3K27me3 is involved in multiple trends of control. H3K4me3, however, mainly focuses on unidirectional regulation. After vernalization most of H3K27me3 changes were kept, but relatively small proportion of H3K4me3 changes could be maintained, as shown by multiple-level analysis, suggesting the active role of H3K27me3 in epigenetic memory. Vernalization-induced histone modification changes were uncovered for VRN3, a gene integrating vernalization/photoperiod signals, suggesting its regulation role at epigenetic level. Memory-related genes were genome-widely identified and a high proportion of them showed quantitative response to vernalization-treatment, suggesting broad existence of this mechanism. Our studies shed new light on epigenetic role of H3K27me3 and VRN3 in vernalization, revealed mechanism underlying epigenetic memory, which helps us to further understand vernalization, a mechanism with great potential in agriculture.

2018-05-22 | GSE93140 | GEO

Temporal expression study of microRNAs in crown tissues of winter wheat grown under natural growth condition

Project description:MicroRNAs (miRNAs) are single strand small non-coding RNAs that regulate target mRNAs at post-transcription level. Winter wheat (Triticum aestivum L.), is an important crop plant all over the world. Long term cold exposure (vernalization) is necessary for winter wheat transition from vegetative growth to reproductive growth, yet the involvement of miRNAs in these stages remains unknown. Therefore, we performed next generation sequencing of small RNAs profiles in crown tissues at three-leaf stage, winter dormancy stage, spring greenup stage and jointing stage.

2021-11-10 | GSE155963 | GEO

Vernalization mediated changes in the Lolium perenne transcriptome

Project description:Falster is a Danish perennial ryegrass ecotype with strong vernalization requirement, while Veyo is an Italian variety with no requirement for vernalization in order to flower. The transcriptome of these two perennial ryegrass genotypes with contrasting vernalization requirements was studied during primary (vernalization and short day conditions), and secondary induction (higher temperature and long day conditions) using an RNA-Seq approach, in order to reveal transcripts with expression profiles indicative of a role in floral induction, both in the promotion and repression of flowering.

2014-09-17 | E-MTAB-2623 | biostudies-arrayexpress

Mechanisms of age-dependent response to winter temperature in perennial flowering of Arabis alpina.

Project description:Transcriptomic profile of Arabis alpina apex enriched material. We compared apices from plants grown for 2 weeks in long days (20M-BM-0C) (juvenile) with apices from plants grown for 8 weeks in long days (20M-BM-0C) (adult) and apices from plants grown for 2 weeks and then shifted in vernalization for 4 weeks with apices from plants grown for 8 weeks and than shifted to vernalization for 4 weeks. 2x2 factorial design. 2 starting ages (2 weeks and 8 weeks) and 2 developmental conditions (before and after vernalization). 4 biological replicates for each condition (16 arrays). Reference: pool of the 16 arrays.

2013-05-27 | E-GEOD-40455 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data